[Bioc-devel] stale link to reposTools in BioC FAQ?

[Herve Pages]

Steven McKinney wrote:
> Hi Herve,
> 
> 
>> -----Original Message-----
>> From: Herve Pages [mailto:hpages at fhcrc.org]
[...]
>> Can you please provide the URLs?
> 
> -------------------------------------------------------------
> reposTools link is on this page:
> http://www.bioconductor.org/docs/faq/
> 
> reposTools 	Tools for dealing with file repositories and allow users to easily install, update, and distribute packages, vignettes, and other files.
> 
> -------------------------------------------------------------
> 
> Another link is on this page:
> http://www.bioconductor.org/whatisit
> 
> The vignettes are generated using the Sweave function from the R package tools. They are documents that intermix text, code, and output (textual and graphical) and can be regenerated automatically whenever the data or analyses change. Additional supporting software for vignettes will aid users in obtaining data and sample code, step through specific analyses, and apply these analyses to their own data (reposTools package).
> 
> -------------------------------------------------------------
> 
> This page still refers to reposTools:
> http://www.bioconductor.org/docs/install-howto.html
> 
> In an R command window, type the following:
> 
> source("http://www.bioconductor.org/biocLite.R")
> biocLite()
> 
> This will install the following subset of packages by default:
> affy 	affydata 	affyPLM
> annaffy 	annotate 	Biobase
> Biostrings 	DynDoc 	gcrma
> genefilter 	geneplotter 	hgu95av2
> limma 	marray 	matchprobes
> multtest 	reposTools 	ROC
> vsn 	xtable
> -------------------------------------------------------------
> 
> Although this page/node states that packages can be updated with bioClite and getBioC,
> the sections describing bioClite and getBioC only discuss installing new
> packages, not updating packages periodically to keep up with changes.
> 
> http://www.bioconductor.org/docs/faq/index.html#For%20Unix/Linux
> 
> Users are encouraged to use biocLite.R or getBioC to obtain, install and update their packages. Information on how to use these functions can be found in the biocLite and getBioC sections of this document.
> 
> 
> 
> -------------------------------------------------------------
> 

Thanks Steven for the useful feedback! I will try to update those pages ASAP.

> 
> 
>>> I just ran an update using
>>>
>>> update.packages(ask = FALSE) ## CRAN updates
>>> update.packages(repos = getOption("BioC.Repos"), ask = FALSE) ## BioC updates
>> Where did you get this code from? Did it work for you?
> 
> I tried various combinations of calls to update.packages, looked in the
> internals of getBioC, getOption, install.packages, etc.  The
> above calls seemed to work best.  Your suggestion below looks better.
> 
> I have not yet determined which function set up list item BioC.Repos
> in my options, information from anyone who knows this would be appreciated.
> 
>> getOption("BioC.Repos")
> [1] "http://www.bioconductor.org/packages/1.9/bioc"            "http://www.bioconductor.org/packages/1.9/data/annotation"
> [3] "http://www.bioconductor.org/packages/1.9/data/experiment" "http://www.bioconductor.org/packages/1.9/omegahat"       


This should be OK too. The CRAN and monograph repos are missing
compared to biocReposList() but, if you don't have any package
from the monograph repo, then doing (in this order):

  > update.packages()

followed by

  > update.packages(getOption("BioC.Repos"))

should be equivalent to

  > update.packages(rep=biocReposList())

Cheers,

H.